12 ms·
Sequencing your DNA with a USB dongle and open source code
- tingletech 6y agoseems pretty impressive. Here is the code linked in the article that does the signal processing to decode the sensor data into DNA sequences. https://github.com/skovaka/UNCALLED https://github.com/skovaka/UNCALLED
- yters 6y agoHow do we get a dongle?
- jmiskovic 6y agoThe source README mentiones supporting MinION ($1000) https://nanoporetech.com/products/minion https://nanoporetech.com/products/minion Nice video here https://www.youtube.com/watch?v=1_mER5qmaVk https://www.youtube.com/watch?v=1_mER5qmaVk Found some previous discusion of HW: https://news.ycombinator.com/item?id=16262719 https://news.ycombinator.com/item?id=16262719 https://news.ycombinator.com/item?id=7893158 https://news.ycombinator.com/item?id=7893158
- deleted 6y ago[deleted]
- snypher 6y agoI think it's misleading for the article to call this a dongle. It's a $1k USB device with expensive consumables, more like a printer.
- Ovah 6y agoAnyone with hands on experience using NanoPore? I've been thinking about buying one of these to play around with. But anecdotally I've heard that they lack utility or are my concerns just myths? a) they are designed to handle many batched samples at once rather than many runs of few samples over time. So in practice they don't really last for many individual samples. b) the computational requirements are high. So while a NanoPore can be plugged into a laptop in the field it would take forever to run the data processing on said computer.
- bioinformatics 6y agoComputational requirements are quite high, but OK if you have good GPUs on hand. A coronavirus sequenced sample on the fast mode without GPUs would take 3-4 hours to complete, while on the high accuracy mode days. GPU access would speed up performance considerably. Error rate for MinIONs is still quite high (10-15%), so a human genome sequencing would be quite inaccurate in some regions. Sequencer is quite cheap, reagents and flow cells are a little bit more expensive.
- Ovah 6y agoThank you. The upfront cost of the sequencer sure makes it tempting at first sight. My desired hobbyist use case is to key out plants, lichens and mushrooms that I find in the field. I have the bioinformatics knowhow just need the hardware. 3-4h seems lika a long time for a genome that is <30k nucleotides long. Mushrooms on average seem to have almost as many genes as coronaviruses has nucleotides. I guess partial sequences (and thus reduced comp time?) might do the trick but it's probably hard to target those partial reference sequences with a long-read method like NanoPore.
- gnramires 6y agoIs the error rate per base pair?
- alwaysdoit 6y agoIf you repeat the process many times will it reduce that error rate, or are the errors non-independent?
- kneel 6y agoNanopores have unacceptably high error rates. Around 10%
- sannee 6y agoIs this an accuracy or precision issue? I am imagining that if you actually have access to the device, you could do as many runs as you want, getting to arbitrarily low error rates.
- dnautics 6y agodon't know why this was downvoted. If I'm not mistaken, there is generally a high error rate per pore fundamentally because it's a single molecule experiment. These get averaged out, but may be difficult to align as it might not necessarily be a straightforward averaging. There are also segments that are fundamentally generally difficult to sequence correctly (single nucleide runs, not even a super high n) that will probably never get satisfyingly resolved no matter how many times you sequence.
- brofallon 6y agoThis is a common misconception - "averaging out" errors only works if the errors are pretty rare at any given site. This is true for some types of errors & sequencing technologies, but not universally true. Some types of DNA sequences (most notably homopolymers and other simple repeats) are very difficult to sequence correctly, and X% of the reads there will be incorrect. If X>20% of so, then it may look like real germline variation no matter how many reads are sequenced
- koeng 6y agoThe errors are non-random. That's why they use machine learning to figure out those errors. You could, of course, also just do traditional statistics on sequences that you want to sequence all the time. I've done that with plasmids before, and it works pretty good. I think there are a few papers on it too.
- searune 6y ago
- u678u 6y agoWow I never thought of this. I understand all the controversy over 23&me and DNA secrecy, but it seems pretty soon it'll be trivial to run DNA anywhere anytime.
- garettmd 6y agoI'm wondering about the impacts of cheap/accessible DNA sequencing in the future. Not just impacts to existing businesses, but what does it mean from a privacy perspective? If someone could take a strand of your hair and then get your genome sequence from it - what would be the implications?
- pishpash 6y agoIn the long future: total loss of privacy and identity as meaningful concepts.
- acwan93 6y agoI was wondering if this would be a solution to the privacy issue that surrounds 23andMe. I would gladly pay a significant amount above $99 (or whatever 23andMe charges) for an offline version of DNA insights.
- RocketSyntax 6y agoMaybe if you ran the test 100 times and did some pileups by position it would be usable in comparison to WGS
- koeng 6y agoIf you want to see what a real run looks like, here is a little gist of my last Nanopore run, raw basecall -> alignment (no consensus) https://gist.github.com/Koeng101/abc674e1acd575646748afcbcc74698d https://gist.github.com/Koeng101/abc674e1acd575646748afcbcc7...
- RocketSyntax 6y agoAlso, this is not new. It's been around for yrs
- dekhn 6y agoschatz periodically dumps PR for attention
- JabavuAdams 6y agoMaybe, but it was a good summary for me and I've been in biophysics for 3 years or so. Also, lots of good keywords and discussion generated here to follow up on. Overall, very useful article and discussion.
- samchorlton 6y agoSo happy to see this here. While sequencing is quite old, mass adoption still has not come. The benefits are clear - faster infectious disease diagnosis, personalized treatment, tracking the spread of infection, identifying food contamination - the use-cases are endless. However before nanopore sequencing came, it was always out of reach of the masses. We've actually started BugSeq[0] to help labs get into nanopore sequencing - improving these open source tools and also writing our own. Orgs like FDA, USDA, big food co's, CDC, etc are now all adopting nanopore sequencing. Happy to see the industry taking off, this will be a step function improvement for public health in general. (disclaimer: founder of BugSeq) 0: https://bugseq.com https://bugseq.com
- dekhn 6y agopersonalized treatment is still best handled by gene panels. nobody has made a compelling argument for WGS for personalized med. Right now it's a huge waste of investment until we understand the multigenicity of diseases better (which is a research problem best solved by sequencing millions of individuals and using high quality WGS sequencers).
- samchorlton 6y agoWe work within the infectious disease space, so I'll give an example from our work that is still personalized medicine: Faster detection of antimicrobial resistance. Every infection will be resistant to different antibacterials/antivirals/antifungals/antiparasitics. What if we could get the patient on the right antimicrobial for their specific infection faster? There's strong evidence that timely administration of correct antimicrobials in septic shock results in improved mortality. Nanopore sequencing very much has the potential to deliver this personalized treatment, without looking at any human genes or panels. If we could rapidly sequence bacteria in the bloodstream and predict their antimicrobial susceptibilities, we can make a difference.
- dekhn 6y agoWhat you're describing is a very reasonable research topic with some supporting evidence. What I'm saying is that nobody has delivered on any of the huge claims about the genome which genomicists made for the last 20 years, specifically in terms of actionable human health. it's time to start calling the bluff.
- koeng 6y agoUntil you also realize you need a Qubit and the library preps and oh now you need NEB next gen enzymes and wow turns out pipette technique really matters. That said, I love Nanopores, I use them in my business, and those error rates you can hack around if you know what’s going on under the hood.
- samchorlton 6y agoExactly. Better analytics can enable this technology to produce better results than competing technologies in less time. Once automated/easy/rapid sample prep comes, there will be mass adoption in the space. Disclaimer: Co-Founder of BugSeq[0] 0: https://bugseq.com https://bugseq.com
- matthew_stone 6y ago> Once automated/easy/rapid sample prep comes, there will be mass adoption in the space. Sounds like Elon calling biology a “software problem”. Not saying that you’re wrong, just saying that the computational folk tend to discount the challenges and skills required in the wet lab.
- samchorlton 6y agoAgreed - Definitely a different class of problem than "software". There are large barriers, eg. lab contamination, biocontainment, low input protocols, etc; however, technological innovation will help with these. That being said, we see a future where someone without advanced molecular training can put a sample (whether that's a nasal swab, concerning white powder received in the mail or lab-grown meat) in a black box and get out a meaningful report.
- phkahler 6y ago>> Not saying that you’re wrong, just saying that the computational folk tend to discount the challenges and skills required in the wet lab. It's time to bring in the industrial automation folks. They probably won't invent a fancy new algorithm to reduce the time to splice the pieces together, but they'll fine tune and automate your reader to the 9's.
- Abishek_Muthian 6y agoThe advancement in DNA sequencing tech for humans, have been a boon for fighting extinction of other animals too. Sequencing bird DNA from feathers to determine their migration and check population was envisioned decades ago and has only been made possible recently to the advancement of the tech. The Bird Genoscape Project[1] was also showcased in this excellent Nat Geo video[2]. [1]https://www.birdgenoscape.org/ https://www.birdgenoscape.org/ [2]https://www.youtube.com/watch?v=_p43ksRgIlk https://www.youtube.com/watch?v=_p43ksRgIlk
- devops000 6y agoCould DNA sequence be used as a private key / seed for a Bitcoin wallet? It does make sense?
- blamestross 6y agoSame problem as all biometrics. Data about you makes for a bad password. It can make an ok username tho.
- CapitalistCartr 6y agoAny password-like object has to be changable. And easily.
- koeng 6y agoAt the 2014 DEFCON Biohacking village I did exactly that. I gave out like 50 tubes of plasmid, all you had to do is go sequence em to extract the private key, and boom, you get like $200 (or like 15K today...) Literally nobody did it for a couple years, so I ended up taking out the bitcoin to pay for more DNA synthesis a few years ago. I actually did delete the bitcoin private key though, so I had to pay for sequencing it back out...
- WanderPanda 6y agoMemorising the seedwords of one key + a backup key in a 1 of 2 multisig setup seem to be a good alternative.
- phkahler 6y agoHow does it handle repeats? I can understand reading AACCCT... since they say the signal depends on several letters. But what about 12 Gs? Or longer runs of the same letter. Is the some way to clock one nucleotide at a time?
- tdido 6y agoNope. You're working with kmers. I think it's 6mers in the current models. It's good because you get redundancy as you move, but coupled with the fact that you can't control dwelling time it makes repetition hard to handle.
- marsdentech 6y agoAs others have said, you're reading a sliding window of k-mers over the target sequence; I think for the MinION k is presently 5. To answer your question directly, it struggles with homopolymer runs, not inherently because they're low complexity, but actually because it's tricky to "clock" how many like, contiguous k-mers have passed through the pore after a given period of time. That is to say, for example, if your target sequence is "GGGGGGG" (i.e. a homopolymer run of 7 Gs), you'd expect to observe three like, contiguous signals (i.e. in current space) for the all-G 5-mer, one signal each per "clock cycle" (which corresponds to the dwell time of the k-mer in the pore). If these "clock cycles" were always constant, it's merely a case of dividing the "time spent on the observed all-G 5-mer" signal by the the "time spent on one clock cycle". Sadly, for our purposes, there's enough wobble in any one such "clock cycle" that that calculation won't always yield a reliable result. The upshot: your "GGGGGGG" (7 Gs) target sequence may be registered as "GGGGGG" (6 Gs) or "GGGGGGGG" (8 Gs), or even something else. Now, for distinguishing two alleles where the difference between them is, say, a doubling in length of an already-very-long homopolymer run, even with the aforementioned "clock wobble", you'd likely be able to see that in MinION data quite clearly. As with all thing DNA sequencing (for the time being, at least!), your precise biological question will determine which (one or more) sequencing techniques are best for the job!
- phkahler 6y agoJust a thought. If the DNA were run through 2 such holes, you could use a nearby non-uniform sequence to clock the reading of the other one. Not a magic bullet, but maybe an improvement. Assumes the readers can be close enough to bound the amount of slack between them, and that they dont interfere with each other.
- lifeisstillgood 6y agoMy first reaction after reaching the halfway point in the article was to check it was not April 1st already. But even on a site like Stackoverflow (hey I can trust Joel right?), and even after coming here and reading "hey yes we build / use those too" I am struggling to believe this. What else don't I know about in biotech? How far ahead is the industry compared to where the average man on the clapham omnibus thinks it is. Please stop the world I want to get off.
- ordu 6y ago> If you try to commercialize it, that takes a while to start a company, and it can take so long that by the time you go to the mechanics of that, the next thing has already emerged. Technological singularity is here! :) [1] https://en.wikipedia.org/wiki/Technological_singularity https://en.wikipedia.org/wiki/Technological_singularity
- unemphysbro 6y agoReally cool to see this here. I worked on solid-state nanopore development as a part of my PhD. Here are some press releases related to articles I published during my PhD: https://physics.illinois.edu/news/article/34064 https://physics.illinois.edu/news/article/34064 https://www.sciencedaily.com/releases/2014/10/141014095320.htm https://www.sciencedaily.com/releases/2014/10/141014095320.h...